Workflow

The workflow

Detailed software versions can be found under Rules.

Results

File Size Description
eRNA
L2.tsv 276 Bytes

Whether L2 is present or not
Quality Control
GM0h.html 632.5 kB
GM12h.html 622.4 kB
GM18h.html 617.3 kB
GM1h.html 615.3 kB
GM24h.html 616.4 kB
GM2h.html 615.4 kB
GM30min.html 626.1 kB
GM48h.html 621.0 kB
GM4h.html 617.9 kB
GM6h.html 624.2 kB
GM72h.html 614.9 kB
GM9h.html 617.5 kB
IMR0h.html 639.8 kB
IMR12h.html 639.4 kB
IMR1h.html 642.0 kB
IMR24h.html 652.9 kB
IMR2h.html 646.1 kB
IMR30min.html 638.6 kB
IMR4h.html 631.0 kB
IMR6h.html 635.8 kB

Statistics

If the workflow has been executed in cluster/cloud, runtimes include the waiting time in the queue.

Rules

Rule Jobs Output Singularity Conda environment
fastqc 20
  • results/2018-10-03/fastqc/GM0h.html
  • results/2018-10-03/fastqc/GM0h.zip
  • results/2018-10-03/fastqc/GM30min.html
  • results/2018-10-03/fastqc/GM30min.zip
  • results/2018-10-03/fastqc/GM1h.html
  • results/2018-10-03/fastqc/GM1h.zip
  • results/2018-10-03/fastqc/GM2h.html
  • results/2018-10-03/fastqc/GM2h.zip
  • results/2018-10-03/fastqc/GM4h.html
  • results/2018-10-03/fastqc/GM4h.zip
  • results/2018-10-03/fastqc/GM6h.html
  • results/2018-10-03/fastqc/GM6h.zip
  • results/2018-10-03/fastqc/GM9h.html
  • results/2018-10-03/fastqc/GM9h.zip
  • results/2018-10-03/fastqc/GM12h.html
  • results/2018-10-03/fastqc/GM12h.zip
  • results/2018-10-03/fastqc/GM18h.html
  • results/2018-10-03/fastqc/GM18h.zip
  • results/2018-10-03/fastqc/GM24h.html
  • results/2018-10-03/fastqc/GM24h.zip
  • results/2018-10-03/fastqc/GM48h.html
  • results/2018-10-03/fastqc/GM48h.zip
  • results/2018-10-03/fastqc/GM72h.html
  • results/2018-10-03/fastqc/GM72h.zip
  • results/2018-10-03/fastqc/IMR0h.html
  • results/2018-10-03/fastqc/IMR0h.zip
  • results/2018-10-03/fastqc/IMR30min.html
  • results/2018-10-03/fastqc/IMR30min.zip
  • results/2018-10-03/fastqc/IMR1h.html
  • results/2018-10-03/fastqc/IMR1h.zip
  • results/2018-10-03/fastqc/IMR2h.html
  • results/2018-10-03/fastqc/IMR2h.zip
  • results/2018-10-03/fastqc/IMR4h.html
  • results/2018-10-03/fastqc/IMR4h.zip
  • results/2018-10-03/fastqc/IMR6h.html
  • results/2018-10-03/fastqc/IMR6h.zip
  • results/2018-10-03/fastqc/IMR12h.html
  • results/2018-10-03/fastqc/IMR12h.zip
  • results/2018-10-03/fastqc/IMR24h.html
  • results/2018-10-03/fastqc/IMR24h.zip
  • fastqc ==0.11.7
GM19_sample_pos2bed 12
  • results/2019-01-28/GM/GM0h_groseq_peak.bed
  • results/2019-01-28/GM/GM30min_groseq_peak.bed
  • results/2019-01-28/GM/GM1h_groseq_peak.bed
  • results/2019-01-28/GM/GM2h_groseq_peak.bed
  • results/2019-01-28/GM/GM4h_groseq_peak.bed
  • results/2019-01-28/GM/GM6h_groseq_peak.bed
  • results/2019-01-28/GM/GM9h_groseq_peak.bed
  • results/2019-01-28/GM/GM12h_groseq_peak.bed
  • results/2019-01-28/GM/GM18h_groseq_peak.bed
  • results/2019-01-28/GM/GM24h_groseq_peak.bed
  • results/2019-01-28/GM/GM48h_groseq_peak.bed
  • results/2019-01-28/GM/GM72h_groseq_peak.bed
  • homer
IMR_sample_pos2bed 8
  • results/2019-01-28/IMR/IMR0h_groseq_peak.bed
  • results/2019-01-28/IMR/IMR30min_groseq_peak.bed
  • results/2019-01-28/IMR/IMR1h_groseq_peak.bed
  • results/2019-01-28/IMR/IMR2h_groseq_peak.bed
  • results/2019-01-28/IMR/IMR4h_groseq_peak.bed
  • results/2019-01-28/IMR/IMR6h_groseq_peak.bed
  • results/2019-01-28/IMR/IMR12h_groseq_peak.bed
  • results/2019-01-28/IMR/IMR24h_groseq_peak.bed
  • homer
test_IMR_vs_Peng 1
  • results/2018-11-10/test/IMR_eRNA_vs_Peng.bed
  • bedtools
test_IMR_vs_GM19 1
  • results/2018-11-10/test/IMR_eRNA_vs_GM19.bed
  • bedtools
test_IMR_vs_liftOver 1
  • results/2018-11-10/test/IMR_eRNA_vs_liftOver.bed
  • bedtools
genes_foldchange 2
  • results/2019-06-26/dge/foldchange/GM19_foldchange.tsv
  • results/2019-06-26/dge/foldchange/IMR_foldchange.tsv
  • matplotlib
  • numpy
  • pandas
eRNA_link_genes 2
  • results/2019-08-26/GM19_link_eRNA.bed
  • results/2019-08-26/IMR_link_eRNA.bed
  • bedtools
eRNA_link_area 1
  • results/2019-08-26/eRNA_viral.bed
  • bedtools
GM19_eRNA_merge_counts 1
  • results/2019-06-03/eRNA/counts/GM19_merged.txt
IMR_eRNA_merge_counts 1
  • results/2019-06-03/eRNA/counts/IMR_merged.txt
eRNA_viral_foldchange 2
  • results/2019-09-27/de/foldchange/GM19_foldchange.tsv
  • results/2019-09-27/de/foldchange/IMR_foldchange.tsv
  • matplotlib
  • numpy
  • pandas
test_eRNA_check_L2 2
  • results/2019-08-26/GM19_L2.bed
  • results/2019-08-26/IMR_L2.bed
  • bedtools
test_homer_check_L2 2
  • results/2019-10-01/GM19_genes_L2.bed
  • results/2019-10-01/IMR_genes_L2.bed
  • bedtools
bed_check_L2 8
  • results/2019-10-06/l2/IMR0h_bam_L2.bed
  • results/2019-10-06/l2/IMR30min_bam_L2.bed
  • results/2019-10-06/l2/IMR1h_bam_L2.bed
  • results/2019-10-06/l2/IMR2h_bam_L2.bed
  • results/2019-10-06/l2/IMR4h_bam_L2.bed
  • results/2019-10-06/l2/IMR6h_bam_L2.bed
  • results/2019-10-06/l2/IMR12h_bam_L2.bed
  • results/2019-10-06/l2/IMR24h_bam_L2.bed
  • bedtools
test_report_L2 1
  • results/2019-10-01/L2.tsv
GM19_sample_findPeaks 12
  • results/2019-01-28/GM/GM0h_groseq_peak.gtf
  • results/2019-01-28/GM/GM30min_groseq_peak.gtf
  • results/2019-01-28/GM/GM1h_groseq_peak.gtf
  • results/2019-01-28/GM/GM2h_groseq_peak.gtf
  • results/2019-01-28/GM/GM4h_groseq_peak.gtf
  • results/2019-01-28/GM/GM6h_groseq_peak.gtf
  • results/2019-01-28/GM/GM9h_groseq_peak.gtf
  • results/2019-01-28/GM/GM12h_groseq_peak.gtf
  • results/2019-01-28/GM/GM18h_groseq_peak.gtf
  • results/2019-01-28/GM/GM24h_groseq_peak.gtf
  • results/2019-01-28/GM/GM48h_groseq_peak.gtf
  • results/2019-01-28/GM/GM72h_groseq_peak.gtf
 docker://emiller88/homer:latest
IMR_sample_findPeaks 8
  • results/2019-01-28/IMR/IMR0h_groseq_peak.gtf
  • results/2019-01-28/IMR/IMR30min_groseq_peak.gtf
  • results/2019-01-28/IMR/IMR1h_groseq_peak.gtf
  • results/2019-01-28/IMR/IMR2h_groseq_peak.gtf
  • results/2019-01-28/IMR/IMR4h_groseq_peak.gtf
  • results/2019-01-28/IMR/IMR6h_groseq_peak.gtf
  • results/2019-01-28/IMR/IMR12h_groseq_peak.gtf
  • results/2019-01-28/IMR/IMR24h_groseq_peak.gtf
 docker://emiller88/homer:latest
IMR_HistonesIntersect 1
  • results/2018-12-02/IMR_eRNA.bed
  • bedtools
GM_hg19_HistonesIntersect 1
  • results/2018-12-02/GM19_eRNA.bed
  • bedtools
GM18_sort_liftOver_Bed 1
  • results/2018-11-10/eRNA_GM_liftover_hg19.sorted.bed
  • bedtools
genes_tpm 2
  • results/2019-06-26/dge/tpm/GM19_tpm.txt
  • results/2019-06-26/dge/tpm/IMR_tpm.txt
  • matplotlib
  • numpy
  • pandas
genes_ripgrep_all 2
  • results/2019-06-26/dge/rg/GM19_de_genes.gtf
  • results/2019-06-26/dge/rg/IMR_de_genes.gtf
  • gawk
  • ripgrep
eRNA_link_merge 1
  • results/2019-08-26/eRNA_merged.bed
  • bedtools
eRNA_link_overlap 1
  • results/2019-08-26/eRNA_overlap_viral.bed
  • bedtools
GM19_eRNA_feature_counts 12
  • results/2019-06-03/eRNA/counts/per_sample/GM0h.txt
  • results/2019-06-03/eRNA/qc/feature_counts/GM0h.txt
  • results/2019-06-03/eRNA/counts/per_sample/GM30min.txt
  • results/2019-06-03/eRNA/qc/feature_counts/GM30min.txt
  • results/2019-06-03/eRNA/counts/per_sample/GM1h.txt
  • results/2019-06-03/eRNA/qc/feature_counts/GM1h.txt
  • results/2019-06-03/eRNA/counts/per_sample/GM2h.txt
  • results/2019-06-03/eRNA/qc/feature_counts/GM2h.txt
  • results/2019-06-03/eRNA/counts/per_sample/GM4h.txt
  • results/2019-06-03/eRNA/qc/feature_counts/GM4h.txt
  • results/2019-06-03/eRNA/counts/per_sample/GM6h.txt
  • results/2019-06-03/eRNA/qc/feature_counts/GM6h.txt
  • results/2019-06-03/eRNA/counts/per_sample/GM9h.txt
  • results/2019-06-03/eRNA/qc/feature_counts/GM9h.txt
  • results/2019-06-03/eRNA/counts/per_sample/GM12h.txt
  • results/2019-06-03/eRNA/qc/feature_counts/GM12h.txt
  • results/2019-06-03/eRNA/counts/per_sample/GM18h.txt
  • results/2019-06-03/eRNA/qc/feature_counts/GM18h.txt
  • results/2019-06-03/eRNA/counts/per_sample/GM24h.txt
  • results/2019-06-03/eRNA/qc/feature_counts/GM24h.txt
  • results/2019-06-03/eRNA/counts/per_sample/GM48h.txt
  • results/2019-06-03/eRNA/qc/feature_counts/GM48h.txt
  • results/2019-06-03/eRNA/counts/per_sample/GM72h.txt
  • results/2019-06-03/eRNA/qc/feature_counts/GM72h.txt
  • subread
IMR_eRNA_feature_counts 8
  • results/2019-06-03/eRNA/counts/per_sample/IMR0h.txt
  • results/2019-06-03/eRNA/qc/feature_counts/IMR0h.txt
  • results/2019-06-03/eRNA/counts/per_sample/IMR30min.txt
  • results/2019-06-03/eRNA/qc/feature_counts/IMR30min.txt
  • results/2019-06-03/eRNA/counts/per_sample/IMR1h.txt
  • results/2019-06-03/eRNA/qc/feature_counts/IMR1h.txt
  • results/2019-06-03/eRNA/counts/per_sample/IMR2h.txt
  • results/2019-06-03/eRNA/qc/feature_counts/IMR2h.txt
  • results/2019-06-03/eRNA/counts/per_sample/IMR4h.txt
  • results/2019-06-03/eRNA/qc/feature_counts/IMR4h.txt
  • results/2019-06-03/eRNA/counts/per_sample/IMR6h.txt
  • results/2019-06-03/eRNA/qc/feature_counts/IMR6h.txt
  • results/2019-06-03/eRNA/counts/per_sample/IMR12h.txt
  • results/2019-06-03/eRNA/qc/feature_counts/IMR12h.txt
  • results/2019-06-03/eRNA/counts/per_sample/IMR24h.txt
  • results/2019-06-03/eRNA/qc/feature_counts/IMR24h.txt
  • subread
eRNA_viral_tpm 2
  • results/2019-09-27/de/tpm/GM19_tpm.txt
  • results/2019-09-27/de/tpm/IMR_tpm.txt
  • matplotlib
  • numpy
  • pandas
homer_meta_pos2bed 2
  • results/2018-11-07/GM19_meta_groseq_peak.bed
  • results/2018-11-07/IMR_meta_groseq_peak.bed
  • homer
IMR_bam_bed 8
  • results/2019-10-06/IMR/IMR0h.bed
  • results/2019-10-06/IMR/IMR30min.bed
  • results/2019-10-06/IMR/IMR1h.bed
  • results/2019-10-06/IMR/IMR2h.bed
  • results/2019-10-06/IMR/IMR4h.bed
  • results/2019-10-06/IMR/IMR6h.bed
  • results/2019-10-06/IMR/IMR12h.bed
  • results/2019-10-06/IMR/IMR24h.bed
  • bedtools
GM19_sample_makeTagDirectory 12
  • results/2019-01-28/GM/GM0h_tagDir
  • results/2019-01-28/GM/GM30min_tagDir
  • results/2019-01-28/GM/GM1h_tagDir
  • results/2019-01-28/GM/GM2h_tagDir
  • results/2019-01-28/GM/GM4h_tagDir
  • results/2019-01-28/GM/GM6h_tagDir
  • results/2019-01-28/GM/GM9h_tagDir
  • results/2019-01-28/GM/GM12h_tagDir
  • results/2019-01-28/GM/GM18h_tagDir
  • results/2019-01-28/GM/GM24h_tagDir
  • results/2019-01-28/GM/GM48h_tagDir
  • results/2019-01-28/GM/GM72h_tagDir
unzip_hg19_uniqmap 1
  • data/2019-07-26/hg19-50nt-uniqmap
IMR_sample_makeTagDirectory 8
  • results/2019-01-28/IMR/IMR0h_tagDir
  • results/2019-01-28/IMR/IMR30min_tagDir
  • results/2019-01-28/IMR/IMR1h_tagDir
  • results/2019-01-28/IMR/IMR2h_tagDir
  • results/2019-01-28/IMR/IMR4h_tagDir
  • results/2019-01-28/IMR/IMR6h_tagDir
  • results/2019-01-28/IMR/IMR12h_tagDir
  • results/2019-01-28/IMR/IMR24h_tagDir
 docker://emiller88/homer:latest
IMR_RemoveGenes 1
  • results/2018-11-09/IMR_groseq_noGenes.bed
  • bedtools
IMR_sort_Histones_Bed 2
  • data/2018-11-13/IMR/IMR_H3K27ac.sorted.bed
  • data/2018-11-13/IMR/IMR_H3K4me1.sorted.bed
  • bedtools
GM19_RemoveGenes 1
  • results/2018-11-09/GM19_meta_groseq_noGenes.bed
  • bedtools
hg19_sort_Histones_Bed 2
  • data/2018-11-13/GM19/GM19_H3K27ac.sorted.bed
  • data/2018-11-13/GM19/GM19_H3K4me1.sorted.bed
  • bedtools
GM18_liftOver_eRNAs 1
  • results/2018-11-10/eRNA_GM_liftover_hg19.bed
  • ucsc-liftover
GM19_merge_counts 1
  • results/2019-06-03/GM19/counts/merged.txt
IMR_merge_counts 1
  • results/2019-06-03/IMR/counts/merged.txt
refSeq 2
  • data/2018-11-09/hg19/genes.gtf
  • data/2018-11-09/hg18/genes.gtf
  • awscli
eRNA_saf_viral 1
  • results/2019-09-27/eRNA_viral.saf
  • pandas
homer_meta_findPeaks 2
  • results/2018-11-07/GM19_meta_transcripts.txt
  • results/2018-11-07/IMR_meta_transcripts.txt
 docker://emiller88/homer:latest
download_hg19_uniqmap 1
  • data/2019-07-26/hg19uniqmap.zip
hg19_fixBEDcoordinates 1
  • data/2018-11-09/hg19/hg19_slop_refseq.sorted.bed
  • bedops
IMR_convert_Histones_to_Bed 2
  • data/2018-11-13/IMR/IMR_H3K27ac.bed
  • data/2018-11-13/IMR/IMR_H3K4me1.bed
  • bedtools
hg19_convert_Histones_to_Bed 2
  • data/2018-11-13/GM19/GM19_H3K27ac.bed
  • data/2018-11-13/GM19/GM19_H3K4me1.bed
  • bedtools
GM18_HistonesIntersect 1
  • results/2018-11-10/GM18_eRNA.bed
  • bedtools
download_mapChain 1
  • data/2018-11-10/hg18ToHg19.over.chain
 docker://continuumio/miniconda3:4.6.14
GM19_feature_counts 11
  • results/2019-06-03/GM19/counts/per_sample/GM0h.txt
  • results/2019-06-03/GM19/qc/feature_counts/GM0h.txt
  • results/2019-06-03/GM19/counts/per_sample/GM30min.txt
  • results/2019-06-03/GM19/qc/feature_counts/GM30min.txt
  • results/2019-06-03/GM19/counts/per_sample/GM1h.txt
  • results/2019-06-03/GM19/qc/feature_counts/GM1h.txt
  • results/2019-06-03/GM19/counts/per_sample/GM2h.txt
  • results/2019-06-03/GM19/qc/feature_counts/GM2h.txt
  • results/2019-06-03/GM19/counts/per_sample/GM4h.txt
  • results/2019-06-03/GM19/qc/feature_counts/GM4h.txt
  • results/2019-06-03/GM19/counts/per_sample/GM6h.txt
  • results/2019-06-03/GM19/qc/feature_counts/GM6h.txt
  • results/2019-06-03/GM19/counts/per_sample/GM9h.txt
  • results/2019-06-03/GM19/qc/feature_counts/GM9h.txt
  • results/2019-06-03/GM19/counts/per_sample/GM12h.txt
  • results/2019-06-03/GM19/qc/feature_counts/GM12h.txt
  • results/2019-06-03/GM19/counts/per_sample/GM18h.txt
  • results/2019-06-03/GM19/qc/feature_counts/GM18h.txt
  • results/2019-06-03/GM19/counts/per_sample/GM24h.txt
  • results/2019-06-03/GM19/qc/feature_counts/GM24h.txt
  • results/2019-06-03/GM19/counts/per_sample/GM48h.txt
  • results/2019-06-03/GM19/qc/feature_counts/GM48h.txt
  • subread
IMR_feature_counts 8
  • results/2019-06-03/IMR/counts/per_sample/IMR0h.txt
  • results/2019-06-03/IMR/qc/feature_counts/IMR0h.txt
  • results/2019-06-03/IMR/counts/per_sample/IMR30min.txt
  • results/2019-06-03/IMR/qc/feature_counts/IMR30min.txt
  • results/2019-06-03/IMR/counts/per_sample/IMR1h.txt
  • results/2019-06-03/IMR/qc/feature_counts/IMR1h.txt
  • results/2019-06-03/IMR/counts/per_sample/IMR2h.txt
  • results/2019-06-03/IMR/qc/feature_counts/IMR2h.txt
  • results/2019-06-03/IMR/counts/per_sample/IMR4h.txt
  • results/2019-06-03/IMR/qc/feature_counts/IMR4h.txt
  • results/2019-06-03/IMR/counts/per_sample/IMR6h.txt
  • results/2019-06-03/IMR/qc/feature_counts/IMR6h.txt
  • results/2019-06-03/IMR/counts/per_sample/IMR12h.txt
  • results/2019-06-03/IMR/qc/feature_counts/IMR12h.txt
  • results/2019-06-03/IMR/counts/per_sample/IMR24h.txt
  • results/2019-06-03/IMR/qc/feature_counts/IMR24h.txt
  • subread
GM19_meta_makeTagDirectory 1
  • results/2018-11-07/GM19_meta_tagDir
IMR_meta_makeTagDirectory 1
  • results/2018-11-07/IMR_meta_tagDir
hg19_slopRefSeq 1
  • data/2018-11-09/hg19/hg19_slop_refseq.bed
  • bedtools
IMR_alignHistones 2
  • data/2018-11-13/IMR/IMR_H3K27ac.bam
  • data/2018-11-13/IMR/IMR_H3K4me1.bam
  • bowtie2 ==2.3.2
  • samtools ==1.5
hg19_alignHistones 2
  • data/2018-11-13/GM19/GM19_H3K27ac.bam
  • data/2018-11-13/GM19/GM19_H3K4me1.bam
  • bowtie2 ==2.3.5
  • samtools ==1.9
hg18_RemoveGenes 1
  • results/2018-11-09/GM18_meta_groseq_noGenes.bed
  • bedtools
GM18_sort_Histones_Bed 2
  • data/2018-11-13/GM18/GM18_H3K27ac.sorted.bed
  • data/2018-11-13/GM18/GM18_H3K4me1.sorted.bed
  • bedtools
refSeq_bed 1
  • data/2018-11-09/hg19/genes.bed
  • awscli
hg19_UCSC_chrom_size 1
  • data/2019-09-25/hg19.chrom.sizes
IMR_H3K27ac_fastq 1
  • data/2018-11-13/IMR_H3K27ac.fastq
 docker://continuumio/miniconda3:4.6.14
IMR_H3K4me1_fastq 1
  • data/2018-11-13/IMR_H3K4me1.fastq
 docker://continuumio/miniconda3:4.6.14
GM_H3K27ac_fastq 1
  • data/2018-11-13/GM_H3K27ac.fastq
GM_H3K4me1_fastq 1
  • data/2018-11-13/GM_H3K4me1.fastq
GM18_meta_pos2bed 1
  • results/2018-11-07/GM18_meta_groseq_peak.bed
  • homer
GM18_convert_Histones_to_Bed 2
  • data/2018-11-13/GM18/GM18_H3K27ac.bed
  • data/2018-11-13/GM18/GM18_H3K4me1.bed
  • bedtools
GM18_meta_findPeaks 1
  • results/2018-11-07/GM18_meta_groseq_peak.gtf
 docker://emiller88/homer:latest
GM18_alignHistones 2
  • data/2018-11-13/GM18/GM18_H3K27ac.bam
  • data/2018-11-13/GM18/GM18_H3K4me1.bam
  • bowtie2 ==2.3.5
  • samtools ==1.9
GM18_meta_makeTagDirectory 1
  • results/2018-11-07/GM18_meta_tagDir
 docker://emiller88/homer:latest